kg_microbe.transform_utils.ontologies_stubs package

Submodules

kg_microbe.transform_utils.ontologies_stubs.ontologies_stubs_transform module

Ontologies-stubs transform.

KG-Microbe deliberately does NOT load the full NCIT, MESH, BTO, PO, or MICRO ontologies — those would each add thousands of unrelated nodes for what is in practice a small per-mapping reference footprint. But the chemical-mapping consolidator and the BacDive isolation-source mapper reference ~73 distinct NCIT IDs, ~95 distinct mesh IDs, a handful of distinct BTO/PO IDs, and ~34 distinct MICRO IDs (across ~150 total reference rows) as canonical xrefs for ingredients, growth media, plant-anatomy isolation sources, and microbial conditions (e.g. NCIT:C29298 'Oatmeal', mesh:D011136 'Tween', PO:0009046 'flower', MICRO:0000082 'nutrient broth'). Without this transform those CURIEs would appear as dangling node ids in the merged KG: edges point at them but no node row carries the label.

This transform:

  1. Calls collect_stub_curies() to discover every NCIT / mesh / BTO / PO / MICRO CURIE referenced anywhere under mappings/.

  2. For each prefix, dispatches on STUB_ONTOLOGY_SOURCES[prefix]["source_type"]:

    • "semsql" — NCIT, mesh, BTO. Queries the local SemSQL DB (data/raw/{ncit,mesh,bto}.db) via OAK and emits one labelled stub node per referenced CURIE; no edges. The mesh entry sets db_prefix = "MESH" to bridge the casing gap between our lowercase mesh: mapping ids and the DB’s uppercase MESH: subject form.

    • "owl_mireot" — PO, MICRO. Runs robot extract --method MIREOT against the source OWL (data/raw/{po,micro}.owl from download.yaml) under a curated upper term and parses the resulting OBO Graph JSON. Emits both nodes (stubs + ancestors up to the upper term, with label/synonyms/xrefs) and biolink:subclass_of edges (one per is_a axiom in the module). MICRO’s two IRI shapes — standard obo/MICRO_xxxx and legacy obo/MicrO.owl/MICRO_xxxx — are handled by passing both forms to ROBOT for every lower term.

  3. Writes per-ontology TSVs to data/transformed/ontologies_stubs/{ncit,mesh,bto,po,micro}_nodes.tsv carrying the canonical KGX node columns. For PO and MICRO, {po,micro}_edges.tsv is also written with the canonical KGX edge columns.

Note for downstream consumers: if a KG built with this transform is ever merged with a kg-microbe-biomedical KG that loads any of these ontologies fully, biolink merge semantics will union nodes — the stub node here is a strict subset of what the full ontology would emit (label/synonym/xref + optional rdfs:subClassOf ancestors), so the union will simply pick the fuller record.

class kg_microbe.transform_utils.ontologies_stubs.ontologies_stubs_transform.OntologiesStubsTransform(input_dir=None, output_dir=None)

Bases: Transform

Emit one labelled stub node per referenced NCIT / mesh / BTO / PO / MICRO CURIE.

DATA_INPUTS: tuple = ('mappings/canonical/chemical_mappings.tsv', 'mappings/canonical/enzyme_mappings.tsv', 'mappings/canonical/enzyme_name_to_go.tsv', 'mappings/canonical/metpo_alias_mappings.tsv', 'mappings/canonical/pathway_mappings.tsv', 'mappings/canonical/phenotype_mappings.tsv', 'mappings/canonical/special_chemical_mappings.tsv', 'mappings/ingredient_mappings.sssom.tsv', 'mappings/isolation_source_to_ontology.tsv', 'mappings/kgmicrobe_unified_entity_mappings.sssom.tsv.gz', 'mappings/madin_environment_id_corrections.tsv')

Derived from the collector’s own list rather than restated, so the two cannot drift (#839). Hand-maintaining it declared 1 of the 11 files this transform reads, which made kgm-freshness-check — which consults nothing but DATA_INPUTS — report the output fresh after a change to any of the other ten. That is the #812 blind spot, and this was the last transform still carrying it.

Note this makes the SSSOM dependency visible: DEFAULT_MAPPING_PATHS[0] is the unified mapping set, so ontologies_stubs is not independent of an incoming MIM release, which the one-file declaration implied it was. Paths outside the repo are skipped rather than raising. This runs at class-definition time, so relative_to raising would surface as an ImportError from a tuple comprehension — breaking every importer, and pointing nowhere near the entry that caused it (#841). An out-of-repo path is not git-checkable anyway, so dropping it loses no signal.

run(data_file=None, **kwargs)

Collect stub CURIEs and emit per-ontology node (and, where configured, edge) TSVs.

Dispatches per STUB_ONTOLOGY_SOURCES source_type:

  • semsql — _write_stub_nodes_from_semsql() writes {prefix}_nodes.tsv only.

  • semsql_mireot — _write_stub_module_from_semsql_walk() writes {prefix}_nodes.tsv AND {prefix}_edges.tsv after walking rdfs:subClassOf ancestors via OAK to the curated upper_terms.

  • owl_mireot — _write_stub_module_from_mireot() writes {prefix}_nodes.tsv AND {prefix}_edges.tsv after running robot extract --method MIREOT against the source OWL.

Parameters:

  • data_file – Unused (kept for the base-class signature). The transform discovers its inputs from the mapping TSVs and the input files in input_base_dir.

  • kwargs – Absorbs forward-compatible kwargs (e.g. show_status) that the transform dispatcher in kg_microbe.transform.transform passes to non-ontologies transforms. The stub transform has no progress bar to toggle, so the flag is intentionally ignored.

Return type:

None

Module contents

Ontologies-stubs transform package.

class kg_microbe.transform_utils.ontologies_stubs.OntologiesStubsTransform(input_dir=None, output_dir=None)

Bases: Transform

Emit one labelled stub node per referenced NCIT / mesh / BTO / PO / MICRO CURIE.

DATA_INPUTS: tuple = ('mappings/canonical/chemical_mappings.tsv', 'mappings/canonical/enzyme_mappings.tsv', 'mappings/canonical/enzyme_name_to_go.tsv', 'mappings/canonical/metpo_alias_mappings.tsv', 'mappings/canonical/pathway_mappings.tsv', 'mappings/canonical/phenotype_mappings.tsv', 'mappings/canonical/special_chemical_mappings.tsv', 'mappings/ingredient_mappings.sssom.tsv', 'mappings/isolation_source_to_ontology.tsv', 'mappings/kgmicrobe_unified_entity_mappings.sssom.tsv.gz', 'mappings/madin_environment_id_corrections.tsv')

Derived from the collector’s own list rather than restated, so the two cannot drift (#839). Hand-maintaining it declared 1 of the 11 files this transform reads, which made kgm-freshness-check — which consults nothing but DATA_INPUTS — report the output fresh after a change to any of the other ten. That is the #812 blind spot, and this was the last transform still carrying it.

Note this makes the SSSOM dependency visible: DEFAULT_MAPPING_PATHS[0] is the unified mapping set, so ontologies_stubs is not independent of an incoming MIM release, which the one-file declaration implied it was. Paths outside the repo are skipped rather than raising. This runs at class-definition time, so relative_to raising would surface as an ImportError from a tuple comprehension — breaking every importer, and pointing nowhere near the entry that caused it (#841). An out-of-repo path is not git-checkable anyway, so dropping it loses no signal.

run(data_file=None, **kwargs)

Collect stub CURIEs and emit per-ontology node (and, where configured, edge) TSVs.

Dispatches per STUB_ONTOLOGY_SOURCES source_type:

  • semsql — _write_stub_nodes_from_semsql() writes {prefix}_nodes.tsv only.

  • semsql_mireot — _write_stub_module_from_semsql_walk() writes {prefix}_nodes.tsv AND {prefix}_edges.tsv after walking rdfs:subClassOf ancestors via OAK to the curated upper_terms.

  • owl_mireot — _write_stub_module_from_mireot() writes {prefix}_nodes.tsv AND {prefix}_edges.tsv after running robot extract --method MIREOT against the source OWL.

Parameters:

  • data_file – Unused (kept for the base-class signature). The transform discovers its inputs from the mapping TSVs and the input files in input_base_dir.

  • kwargs – Absorbs forward-compatible kwargs (e.g. show_status) that the transform dispatcher in kg_microbe.transform.transform passes to non-ontologies transforms. The stub transform has no progress bar to toggle, so the flag is intentionally ignored.

Return type:

None